Tuesday, July 28, 2015

What to avoid when making an identification key, continued

Currently I am reading a very long taxonomic paper. Not making a lot of progress due to various unrelated issues, but even only less than a fifth in I already notice several cardinal sins of identification keys. This is like another list of how not to do it:

Thursday, July 23, 2015

Botany picture #209: Lecanora subfarinacea

This, I was told, is Lecanora subfarinacea, another lichen that I photographed in central Tasmania in 2013. While fruticose and foliose lichens can look even more alien compared to true plants, I somehow still like crustose species best. And although I generally lean more towards the convergence rather than the contingency view of evolutionary biology, they certainly show a completely different solution to the problem of being a photosynthetic organism on land. (In this case a partnership of two organisms, of course.)

It is easy to imagine that land plants with different pigmentation could have evolved on other planets, especially if their sun isn't exactly the same colour as ours (orange stars are supposedly even better for life than yellow ones). Not least because we already have brown, yellow-brown and red algae on this planet. The much bigger question is if there could be planets where something like Eukaryotes evolves but, because contingency etc. etc., there are never going to be any vascular plant or even bryophyte equivalents.

I find that hard to conceive - the advantage of getting taller to shade and overgrow competitors seems to big, and all it needs is enough time for one lineage to make the first step into that direction - but who knows? Maybe there are other planets out there in deep space that have all the land covered only with crusts like the above.

Monday, July 20, 2015

Botany picture #208: Rhizocarpa geographica

Another lichen from Tasmania in 2012: Rhizocarpa geographica. Or at least so I was told, but a quick Google search seems to confirm it.

Friday, July 17, 2015

Parsimony Analysis of Endemism and similar

Quiiiite some time ago now I started a little series on the uses of parsimony in systematics, evolutionary biology and biogeography, and then kind of dropped the ball before coming to the biogeography part. Having recently read a few more papers on methods in biogeography, this seems like an opportune time to pick the thread up again.

Specifically, I came across an approach that was apparently very popular in the early noughties but then seems to have disappeared again: Parsimony Analysis of Endemicity (PAE; e.g. Nihei, 2006) and its variant Cladistic Analysis of Distributions and Endemism (CADE; e.g. Porzecanski & Cracraft, 2005).

But before I consider if PAE is worth trying out, it would be interesting to know what it is supposed to be good for, and for that let's consider...

What is biogeography about?

This is actually not an easy question to answer. I mean, it is very simple for phylogenetics (inferring relationships between species) or taxonomy (naming and classifying groups of organisms), but certain other fields like ecology or evolutionary biology are much more complex, broad and fuzzy. And biogeography is one of them, at least in my eyes.

At a minimum, biogeography as a discipline seems to encompass all of the following:

Sunday, July 12, 2015

White snow and a white fungus

Today I and three colleagues scouted the vegetation of the Australian National University's coastal Kioloa Campus in preparation for a field trip. Because I will probably write about the area when we go back there with the students, and because the weather was pretty dreary anyway, I will refrain from posting lots of pictures now.

However, on the way between Canberra and Bungendore we ran into snow, a rare phenomenon at this elevation in Australia.

Yes, similar photos have probably appeared on the social media accounts of thousands of Australians today, but no matter.

Although as implied above the light conditions were far from ideal, I tried to take a few pictures at Kioloa, and at least the following one turned out reasonably nice, perhaps because its object is very bright itself:

Note the finely reticulate structure of the fruiting bodies. Sadly I don't know the name of this fungus. Even Celeste, the mycologist of our party, said she would have to look it up.

Saturday, July 11, 2015

Botany picture #207: Usnea torulosa

Still not much to write about, but I recently discovered a few pictures of Tasmanian lichens that the local colleagues had given me names for. I have never done any science to them, but lichens are really interesting, both for their weird shapes and colours and their ability to grow under very hostile conditions. The above is apparently Usnea torulosa, Tasmania, 2012. At least the genus is no surprise, in this growth form it is fairly easy to recognise.

Monday, July 6, 2015

Botany picture #206: Meconopsis betonicifolia

Meconopsis betonicifolia (Papaveraceae) Botanic Garden of Zurich, 2010. A nice blue poppy, not much to add here.

Thursday, July 2, 2015

Variants of peer review

In my field of science, peer review generally takes the following form: You submit a manuscript to a journal, it is reviewed by two to three colleagues, and then the editor of the journal decides whether to publish, whether to request changes before re-examining the paper for publication, or whether to reject. The editor and the peer reviewers know who wrote the paper, but you don't usually know who the reviewers were.

There are other ways of doing this; they have their own advantages and disadvantages, but I definitely know how I would change things if I could.

One often heard suggestion lately is that peer review should be "open" (or public); that is, the authors should be informed who the reviewers were. As far as I can see, there are two main considerations behind this. First, that this will make it harder to be unfair and rude, which is of course much easier to be under our current system. Second, a general and in this particular case unwarranted infatuation with the concept of openness, as in open source software or open access publishing.

Because there is one very simple problem: If the author can see who suggested their paper be rejected, will that not have a severely chilling effect? Imagine a postdoc reviewing the manuscript of a very influential professor, for example. Will they dare to say something negative if they know their name will be connected with it, be it ever so justified? I am fairly sure that I at least would say no considerably more often if I were to asked to review papers under an open system. Who knows when I would offend somebody who has to decide about my grant application a year later?

Wednesday, July 1, 2015

Botany picture #205: Coprosma hirtella

Wanted to write something, but too tired now. Instead: Coprosma hirtella (Rubiaceae), Australian Capital Territory, 2015. Again, as a German one gets a very lopsided view of the Rubiaceae family because it is mostly represented in Europe with scraggly herbs bearing pseudo-verticllate leaves. Most species of the family, which by the way is one of the ten largest flowering plant families, are actually woody and have opposite leaves.

This is from our little day trip to Mount Franklin Road in Namadgi National Park in late summer, the same where we saw the Royal Bluebell.